5D9Q

Crystal Structure of the BG505 SOSIP gp140 HIV-1 Env trimer in Complex with the Broadly Neutralizing Fab PGT122 and scFv NIH45-46

PDB DOI: https://doi.org/10.2210/pdb5D9Q/pdb

Classification: IMMUNE SYSTEM
Organism(s): Human immunodeficiency virus 1, Homo sapiens
Expression System: Homo sapiens
Mutation(s): No

Deposited: 2015-08-18 Released: 2016-08-17
Deposition Author(s): Julien, J.-P., Stanfield, R.L., Ward, A.B., Wilson, I.A.
Funding Organization(s): National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID), International AIDS Vaccine Initiative, Bill & Melinda Gates Foundation

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 4.40 Å
R-Value Free: 0.320
R-Value Work: 0.290
R-Value Observed: 0.290

wwPDB Validation 3D Report Full Report

This is version 3.2 of the entry. See complete history.

Macromolecule Content

Total Structure Weight: 473.37 kDa
Atom Count: 31,374
Modelled Residue Count: 3,678
Deposited Residue Count: 3,933
Unique protein chains: 5

Macromolecules

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(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Envelope glycoprotein gp120	A [auth G], F [auth A], K [auth J]	472	Human immunodeficiency virus 1	Mutation(s): 0 Gene Names: env
UniProt
Find proteins for Q2N0S6 (Human immunodeficiency virus 1) Explore Q2N0S6 Go to UniProtKB: Q2N0S6
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	Q2N0S6
Sequence Annotations Expand
Reference Sequence

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Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Envelope glycoprotein gp41	B, G [auth C], L [auth K]	152	Human immunodeficiency virus 1	Mutation(s): 0 Gene Names: env
UniProt
Find proteins for Q2N0S6 (Human immunodeficiency virus 1) Explore Q2N0S6 Go to UniProtKB: Q2N0S6
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	Q2N0S6
Sequence Annotations Expand
Reference Sequence

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Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
PGT122 light chain,Ig lambda-3 chain C regions	C [auth L], H [auth E], M	211	Homo sapiens	Mutation(s): 0
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
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Reference Sequence

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Entity ID: 4
Molecule	Chains	Sequence Length	Organism	Details	Image
PGT122 heavy chain,IgG H chain	D [auth H], I [auth F], N	235	Homo sapiens	Mutation(s): 0
UniProt
Find proteins for S6B291 (Homo sapiens) Explore S6B291 Go to UniProtKB: S6B291
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	S6B291
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Reference Sequence

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Entity ID: 5
Molecule	Chains	Sequence Length	Organism	Details	Image
NIH45-46 single chain Fv	E [auth D], J [auth I], O	241	Homo sapiens	Mutation(s): 0
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
Sequence Annotations Expand
Reference Sequence

Oligosaccharides

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Entity ID: 6
Molecule	Chains	Length	2D Diagram	Glycosylation	3D Interactions
alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-6)]beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose	DA [auth d], FA [auth f], JA [auth j], P, R, DA [auth d], FA [auth f], JA [auth j], P, R, RA [auth r], TA [auth t], V, XA [auth x]	5		N-Glycosylation	Interactions Focus chain DA [auth d] Focus chain FA [auth f] Focus chain JA [auth j] Focus chain P Focus chain R Focus chain RA [auth r] Focus chain TA [auth t] Focus chain V Focus chain XA [auth x] Interactions & Density Focus chain DA [auth d] Focus chain FA [auth f] Focus chain JA [auth j] Focus chain P Focus chain R Focus chain RA [auth r] Focus chain TA [auth t] Focus chain V Focus chain XA [auth x]
Glycosylation Resources
GlyTouCan: G22768VO GlyCosmos: G22768VO GlyGen: G22768VO

Entity ID: 7
Molecule	Chains	Length	2D Diagram	Glycosylation	3D Interactions
alpha-D-mannopyranose-(1-3)-beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose	EA [auth e], Q, SA [auth s]	4		N-Glycosylation	Interactions Focus chain EA [auth e] Focus chain Q Focus chain SA [auth s] Interactions & Density Focus chain EA [auth e] Focus chain Q Focus chain SA [auth s]
Glycosylation Resources
GlyTouCan: G81315DD GlyCosmos: G81315DD GlyGen: G81315DD

Entity ID: 8
Molecule	Chains	Length	2D Diagram	Glycosylation	3D Interactions
2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose	AA [auth a], BA [auth b], BB [auth 1], CA [auth c], CB [auth 2], AA [auth a], BA [auth b], BB [auth 1], CA [auth c], CB [auth 2], DB [auth 3], EB [auth 4], GA [auth g], KA [auth k], NA [auth n], OA [auth o], PA [auth p], QA [auth q], S, UA [auth u], W, YA [auth y], Z	2		N-Glycosylation	Interactions Focus chain AA [auth a] Focus chain BA [auth b] Focus chain BB [auth 1] Focus chain CA [auth c] Focus chain CB [auth 2] Focus chain DB [auth 3] Focus chain EB [auth 4] Focus chain GA [auth g] Focus chain KA [auth k] Focus chain NA [auth n] Focus chain OA [auth o] Focus chain PA [auth p] Focus chain QA [auth q] Focus chain S Focus chain UA [auth u] Focus chain W Focus chain YA [auth y] Focus chain Z Interactions & Density Focus chain AA [auth a] Focus chain BA [auth b] Focus chain BB [auth 1] Focus chain CA [auth c] Focus chain CB [auth 2] Focus chain DB [auth 3] Focus chain EB [auth 4] Focus chain GA [auth g] Focus chain KA [auth k] Focus chain NA [auth n] Focus chain OA [auth o] Focus chain PA [auth p] Focus chain QA [auth q] Focus chain S Focus chain UA [auth u] Focus chain W Focus chain YA [auth y] Focus chain Z
Glycosylation Resources
GlyTouCan: G42666HT GlyCosmos: G42666HT GlyGen: G42666HT

Entity ID: 9
Molecule	Chains	Length	2D Diagram	Glycosylation	3D Interactions
alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-6)]alpha-D-mannopyranose-(1-6)-[alpha-D-mannopyranose-(1-3)]beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose	HA [auth h], LA [auth l], T, VA [auth v], X, HA [auth h], LA [auth l], T, VA [auth v], X, ZA [auth z]	7		N-Glycosylation	Interactions Focus chain HA [auth h] Focus chain LA [auth l] Focus chain T Focus chain VA [auth v] Focus chain X Focus chain ZA [auth z] Interactions & Density Focus chain HA [auth h] Focus chain LA [auth l] Focus chain T Focus chain VA [auth v] Focus chain X Focus chain ZA [auth z]
Glycosylation Resources
GlyTouCan: G55220VL GlyCosmos: G55220VL GlyGen: G55220VL

Entity ID: 10
Molecule	Chains	Length	2D Diagram	Glycosylation	3D Interactions
alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose-(1-6)]alpha-D-mannopyranose-(1-6)]beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose	IA [auth i], U, WA [auth w]	11		N-Glycosylation	Interactions Focus chain IA [auth i] Focus chain U Focus chain WA [auth w] Interactions & Density Focus chain IA [auth i] Focus chain U Focus chain WA [auth w]
Glycosylation Resources
GlyTouCan: G60230HH GlyCosmos: G60230HH GlyGen: G60230HH

Entity ID: 11
Molecule	Chains	Length	2D Diagram	Glycosylation	3D Interactions
alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-6)]alpha-D-mannopyranose-(1-6)]beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose	AB [auth 0], MA [auth m], Y	10		N-Glycosylation	Interactions Focus chain AB [auth 0] Focus chain MA [auth m] Focus chain Y Interactions & Density Focus chain AB [auth 0] Focus chain MA [auth m] Focus chain Y
Glycosylation Resources
GlyTouCan: G91704UR GlyCosmos: G91704UR GlyGen: G91704UR

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
NAG Query on NAG Download Ideal Coordinates CCD File SDF format, chain FB [auth G] SDF format, chain GB [auth G] SDF format, chain HB [auth G] SDF format, chain IB [auth G] SDF format, chain JB [auth B] SDF format, chain KB [auth B] SDF format, chain LB [auth A] SDF format, chain MB [auth A] SDF format, chain NB [auth A] SDF format, chain OB [auth A] SDF format, chain PB [auth C] SDF format, chain QB [auth C] SDF format, chain RB [auth J] SDF format, chain SB [auth J] SDF format, chain TB [auth J] SDF format, chain UB [auth J] SDF format, chain VB [auth K] SDF format, chain WB [auth K] MOL2 format, chain FB [auth G] MOL2 format, chain GB [auth G] MOL2 format, chain HB [auth G] MOL2 format, chain IB [auth G] MOL2 format, chain JB [auth B] MOL2 format, chain KB [auth B] MOL2 format, chain LB [auth A] MOL2 format, chain MB [auth A] MOL2 format, chain NB [auth A] MOL2 format, chain OB [auth A] MOL2 format, chain PB [auth C] MOL2 format, chain QB [auth C] MOL2 format, chain RB [auth J] MOL2 format, chain SB [auth J] MOL2 format, chain TB [auth J] MOL2 format, chain UB [auth J] MOL2 format, chain VB [auth K] MOL2 format, chain WB [auth K]	FB [auth G] GB [auth G] HB [auth G] IB [auth G] JB [auth B] FB [auth G], GB [auth G], HB [auth G], IB [auth G], JB [auth B], KB [auth B], LB [auth A], MB [auth A], NB [auth A], OB [auth A], PB [auth C], QB [auth C], RB [auth J], SB [auth J], TB [auth J], UB [auth J], VB [auth K], WB [auth K]	2-acetamido-2-deoxy-beta-D-glucopyranose C₈ H₁₅ N O₆ OVRNDRQMDRJTHS-FMDGEEDCSA-N		Interactions Focus chain FB [auth G] Focus chain GB [auth G] Focus chain HB [auth G] Focus chain IB [auth G] Focus chain JB [auth B] Focus chain KB [auth B] Focus chain LB [auth A] Focus chain MB [auth A] Focus chain NB [auth A] Focus chain OB [auth A] Focus chain PB [auth C] Focus chain QB [auth C] Focus chain RB [auth J] Focus chain SB [auth J] Focus chain TB [auth J] Focus chain UB [auth J] Focus chain VB [auth K] Focus chain WB [auth K] Interactions & Density Focus chain FB [auth G] Focus chain GB [auth G] Focus chain HB [auth G] Focus chain IB [auth G] Focus chain JB [auth B] Focus chain KB [auth B] Focus chain LB [auth A] Focus chain MB [auth A] Focus chain NB [auth A] Focus chain OB [auth A] Focus chain PB [auth C] Focus chain QB [auth C] Focus chain RB [auth J] Focus chain SB [auth J] Focus chain TB [auth J] Focus chain UB [auth J] Focus chain VB [auth K] Focus chain WB [auth K]

Modified Residues 1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
PCA Query on PCA	E [auth D], J [auth I], O	L-PEPTIDE LINKING	C₅ H₇ N O₃		GLN

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 4.40 Å
R-Value Free: 0.320
R-Value Work: 0.290
R-Value Observed: 0.290
Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 153.76	α = 90
b = 254.35	β = 100.96
c = 283.55	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
XDS	data reduction
XDS	data scaling
PHASER	phasing

Structure Validation

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Entry History & Funding Information

Deposition Data

Released Date: 2016-08-17

Deposition Author(s):

Funding Organization	Location	Grant Number
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)	United States	P01 AI82362
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)	United States	R01 AI084817
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)	United States	CHAVI-ID 1UM1AI100663
International AIDS Vaccine Initiative	United States	--
Bill & Melinda Gates Foundation	United States	--

Revision History (Full details and data files)

Version 1.0: 2016-08-17
Type: Initial release
Version 1.1: 2016-09-07
Changes: Database references
Version 1.2: 2017-09-06
Changes: Author supporting evidence, Derived calculations
Version 2.0: 2019-12-11
Changes: Author supporting evidence, Polymer sequence
Version 3.0: 2020-07-29
Type: Remediation
Reason: Carbohydrate remediation
Changes: Atomic model, Data collection, Derived calculations, Experimental preparation, Structure summary
Version 3.1: 2022-03-16
Changes: Author supporting evidence, Database references, Derived calculations, Structure summary
Version 3.2: 2023-09-27
Changes: Data collection, Refinement description

RCSB PDB Core Operations are funded by the National Science Foundation (DBI-1832184), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM133198.

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5D9Q

Crystal Structure of the BG505 SOSIP gp140 HIV-1 Env trimer in Complex with the Broadly Neutralizing Fab PGT122 and scFv NIH45-46

Entity ID: 1

UniProt

Entity Groups

Sequence Annotations

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Entity ID: 2

UniProt

Entity Groups

Sequence Annotations

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Entity ID: 3

Entity Groups

Sequence Annotations

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Entity ID: 4

UniProt

Entity Groups

Sequence Annotations

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Entity ID: 5

Entity Groups

Sequence Annotations

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Entity ID: 6

Glycosylation Resources

Entity ID: 7

Glycosylation Resources

Entity ID: 8

Glycosylation Resources

Entity ID: 9

Glycosylation Resources

Entity ID: 10

Glycosylation Resources

Entity ID: 11

Glycosylation Resources

Experimental Data

Structure Validation

Deposition Data

Revision History (Full details and data files)